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https://www.readbyqxmd.com/read/27936442/label-free-colorimetric-detection-of-cancer-related-gene-based-on-two-step-amplification-of-molecular-machine
#1
Huo Xu, Dong Wu, Chen-Qiao Li, Zheng Lu, Xiao-Yun Liao, Jie Huang, Zai-Sheng Wu
Highly sensitive detection of K-ras gene is of great significance in biomedical research and clinical diagnosis. Here, we developed a colorimetric biosensing system for the detection of proto-oncogene K-ras based on enhanced amplification effect of DNA molecular machine, where dual isothermal circular strand-displacement amplification (D-SDA) occurs on two arms in one-to-one correspondence. Specifically, we designed a primer-locked hairpin probe (HP) and a primer-contained linear polymerization template (PPT)...
December 2, 2016: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/27935692/dynamic-and-electrostatic-effects-on-the-reaction-catalyzed-by-hiv-1-protease
#2
Agnieszka Krzemińska, Vicent Moliner, Katarzyna Świderek
HIV-1 Protease (HIV-1 PR) is one of the three enzymes essential for the replication process of HIV-1 virus, which explains why it has been the main target for design of drugs against acquired immunodeficiency syndrome (AIDS). This work is focused on exploring the proteolysis reaction catalyzed by HIV-1 PR, with special attention to the dynamic and electrostatic effects governing its catalytic power. Free energy surfaces for all possible mechanisms have been computed in terms of potentials of mean force (PMFs) within hybrid QM/MM potentials, with the QM subset of atoms described at semiempirical (AM1) and DFT (M06-2X) level...
December 9, 2016: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/27935295/a-metabolism-based-click-mediated-platform-for-specific-imaging-and-quantification-of-cell-surface-sialic-acids
#3
Yong Liang, Xin Jiang, Rong Yuan, Yang Zhou, Caixia Ji, Limin Yang, Haifeng Chen, Qiuquan Wang
Although we believe that the cell surface sialic acids (Sias) are playing an important role in cell-cell interactions and related tumor metastasis processes, acquisition of their quantitative information has yet been a challenge to date. Here, we reported the construction of a new analytical platform for Sias-specific imaging and quantification. We used N-Azidoacetyl-Mannosamine tetraacylated as a metabolic sugar substrate to bioassemble azido-Sias on the surface of cells via the metabolic pathway of Sias de novo synthesis...
December 9, 2016: Analytical Chemistry
https://www.readbyqxmd.com/read/27934432/reactivity-of-a-cobalt-iii-hydroperoxo-complex-in-electrophilic-reactions
#4
Bongki Shin, Kyle D Sutherlin, Takehiro Ohta, Takashi Ogura, Edward I Solomon, Jaeheung Cho
The reactivity of mononuclear metal-hydroperoxo adducts has fascinated researchers in many areas due to their diverse biological and catalytic processes. In this study, a mononuclear cobalt(III)-peroxo complex bearing a tetradentate macrocyclic ligand, [Co(III)(Me3-TPADP)(O2)](+) (Me3-TPADP = 3,6,9-trimethyl-3,6,9-triaza-1(2,6)-pyridinacyclodecaphane), was prepared by reacting [Co(II)(Me3-TPADP)(CH3CN)2](2+) with H2O2 in the presence of triethylamine. Upon protonation, the cobalt(III)-peroxo intermediate was converted into a cobalt(III)-hydroperoxo complex, [Co(III)(Me3-TPADP)(O2H)(CH3CN)](2+)...
December 5, 2016: Inorganic Chemistry
https://www.readbyqxmd.com/read/27934294/label-free-proteomic-reveals-that-cowpea-severe-mosaic-virus-transiently-suppresses-the-host-leaf-protein-accumulation-during-the-compatible-interaction-with-cowpea-vigna-unguiculata-l-walp
#5
Ana L S Paiva, Jose T A Oliveira, Gustavo A de Souza, Ilka M Vasconcelos
Viruses are important plant pathogens that threaten diverse crops worldwide. Diseases caused by Cowpea severe mosaic virus (CPSMV) have drawn attention because of the serious damages they cause to economically important crops including cowpea. This work was undertaken to quantify and identify the responsive proteins of a susceptible cowpea genotype infected with CPSMV, in comparison with mock-inoculated controls, using label-free quantitative proteomics and databanks, aiming at providing insights on the molecular basis of this compatible interaction...
December 2, 2016: Journal of Proteome Research
https://www.readbyqxmd.com/read/27934126/selective-and-sensitive-monitoring-of-cerebral-antioxidants-based-on-the-dye-labeled-dna-polydopamine-conjugates
#6
Shishi Ma, Yan-Xia Qi, Xiao-Qin Jiang, Jie-Qiong Chen, Qiao-Yu Zhou, Guoyue Shi, Min Zhang
A simple and novel method for evaluating antioxidants in complex biological fluids has been developed based on the interaction of dye-labeled single-strand DNA (ssDNA) and polydopamine (PDA). Due to the interaction between ssDNA and PDA, the fluorescence of dye-labeled ssDNA (e.g., FITC-ssDNA, as donor) can be quenched by PDA (as acceptor) to the fluorescence "off" state through Förster resonance energy transfer (FRET). However, in the presence of various antioxidants, such as glutathione (GSH), ascorbic acid (AA), cysteine (Cys), and homocysteine (Hcys), the spontaneous oxidative polymerization reaction from DA to PDA would be blocked, resulting in the freedom of FITC-ssDNA and leading to the fluorescence "on" state...
December 6, 2016: Analytical Chemistry
https://www.readbyqxmd.com/read/27934114/hybrid-synthetic-receptors-on-mosfet-devices-for-detection-of-prostate-specific-antigen-in-human-plasma
#7
Vibha K Tamboli, Nikhil Bhalla, Pawan Jolly, Chris R Bowen, John T Taylor, Jenna L Bowen, Chris J Allender, Pedro Estrela
The study reports the use of extended gate field-effect transistors (FET) for the label-free and sensitive detection of prostate cancer (PCa) biomarkers in human plasma. The approach integrates for the first time hybrid synthetic receptors comprising of highly selective aptamer-lined pockets (apta-MIP) with FETs for sensitive detection of prostate specific antigen (PSA) at clinically relevant concentrations. The hybrid synthetic receptors were constructed by immobilizing an aptamer-PSA complex on gold and subjecting it to 13 cycles of dopamine electropolymerization...
December 6, 2016: Analytical Chemistry
https://www.readbyqxmd.com/read/27934107/detection-of-prostate-specific-membrane-antigen-at-picomolar-levels-using-biocatalysis-coupled-to-assisted-ion-transfer-voltammetry-at-a-liquid-organogel-microinterface-array
#8
Rashida Akter, Damien W M Arrigan
A label-free electrochemical strategy for the detection of a cancer biomarker, prostate specific membrane antigen (PSMA), at picomolar concentrations without the use of antibodies, was investigated. The approach is based on the assisted ion transfer of protons, generated by a series of enzymatic reactions, at an array of microinterfaces between two immiscible electrolyte solutions (μ-ITIES). This nonredox electrochemical approach based on biocatalysis-coupled proton transfer at the μ-ITIES array opens a new way to detect the prostate cancer biomarker, with detection capability achieved at concentrations below those indicative of disease presence...
December 6, 2016: Analytical Chemistry
https://www.readbyqxmd.com/read/27934101/exploiting-surface-plasmon-enhanced-light-scattering-for-the-design-of-ultrasensitive-biosensing-modality
#9
Chih-Tsung Yang, Lin Wu, Xiaohu Liu, Nhung Thi Tran, Ping Bai, Bo Liedberg, Yi Wang, Benjamin Thierry
Development of new detection methodologies and amplification schemes is indispensable for plasmonic biosensors to improve the sensitivity for the detection of trace amounts of analytes. Herein, an ultrasensitive scheme for signal enhancement based on the concept of surface-plasmon-resonance-enhanced light scattering (SP-LS) was validated experimentally and theoretically. The SP-LS of gold nanoparticles' (AuNPs) tags was employed in a sandwich assay for the detection of cardiac troponin I and provided up to 2 orders of magnitude improved sensitivity over conventional AuNPs-enhanced refractometric measurements and 3 orders of magnitude improvement over label-free SPR...
December 6, 2016: Analytical Chemistry
https://www.readbyqxmd.com/read/27934087/a-multifunctional-platform-for-tumor-angiogenesis-targeted-chemo-thermal-therapy-using-polydopamine-coated-gold-nanorods
#10
Lu Zhang, Huilan Su, Jiali Cai, Dengfeng Cheng, Yongjie Ma, Jianping Zhang, Chuanqing Zhou, Shiyuan Liu, Hongcheng Shi, Yingjian Zhang, Chunfu Zhang
Image-guided combined chemo-thermal therapy assists in optimizing treatment time, enhancing therapeutic efficiency, and circumventing side effects. In the present study, we developed a chemo-photothermal theranostic platform based on polydopamine (PDA)-coated gold nanorods (GNRs). The PDA coating was thin; however, it significantly suppressed the cytotoxicity of the cetyltrimethylammonium bromide template and allowed high cisplatin loading efficiency, arginine-glycine-aspartic acid (RGD) peptide (c(RGDyC)) conjugation, and chelator-free iodine-125 labeling (RGD-(125)IPt-PDA@GNRs)...
November 22, 2016: ACS Nano
https://www.readbyqxmd.com/read/27934084/highly-sensitive-and-quick-detection-of-acute-myocardial-infarction-biomarkers-using-in2o3-nanoribbon-biosensors-fabricated-using-shadow-masks
#11
Qingzhou Liu, Noppadol Aroonyadet, Yan Song, Xiaoli Wang, Xuan Cao, Yihang Liu, Sen Cong, Fanqi Wu, Mark E Thompson, Chongwu Zhou
We demonstrate a scalable and facile lithography-free method for fabricating highly uniform and sensitive In2O3 nanoribbon biosensor arrays. Fabrication with shadow masks as the patterning method instead of conventional lithography provides low-cost, time-efficient, and high-throughput In2O3 nanoribbon biosensors without photoresist contamination. Combined with electronic enzyme-linked immunosorbent assay for signal amplification, the In2O3 nanoribbon biosensor arrays are optimized for early, quick, and quantitative detection of cardiac biomarkers in diagnosis of acute myocardial infarction (AMI)...
November 22, 2016: ACS Nano
https://www.readbyqxmd.com/read/27934066/nanopores-and-nanochannels-from-gene-sequencing-to-genome-mapping
#12
Stefan Howorka, Zuzanna Siwy
DNA strands can be analyzed at the single-molecule level by isolating them inside nanoscale holes. The strategy is used for the label-free and portable sequencing with nanopores. Nanochannels can also be applied to map genomes with high resolution, as shown by Jeffet et al. in this issue of ACS Nano. Here, we compare the two strategies in terms of biophysical similarities and differences and describe that both are complementary and can improve the DNA analysis for genomic research and diagnostics.
November 22, 2016: ACS Nano
https://www.readbyqxmd.com/read/27932699/a-systematic-investigation-of-the-best-buffers-for-use-in-screening-by-maldi-mass-spectrometry
#13
Jessica Chandler, Carl Haslam, Neil Hardy, Melanie Leveridge, Peter Marshall
Matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) offers a label-free alternative for the screening of biochemical targets in both 1536- and 6144-assay formats, as well as potentially providing increased sensitivity, reproducibility, and the simultaneous detection of multiple assay components within a specified m/z range. Ion suppression effects are one of the principal limitations reported for MS analysis. Within MALDI-MS screening, it has been identified that certain biochemical components incorporated into the assay (e...
December 8, 2016: Journal of Biomolecular Screening
https://www.readbyqxmd.com/read/27930344/specific-detection-of-biomolecules-in-physiological-solutions-using-graphene-transistor-biosensors
#14
Ning Gao, Teng Gao, Xiao Yang, Xiaochuan Dai, Wei Zhou, Anqi Zhang, Charles M Lieber
Nanomaterial-based field-effect transistor (FET) sensors are capable of label-free real-time chemical and biological detection with high sensitivity and spatial resolution, although direct measurements in high-ionic-strength physiological solutions remain challenging due to the Debye screening effect. Recently, we demonstrated a general strategy to overcome this challenge by incorporating a biomolecule-permeable polymer layer on the surface of silicon nanowire FET sensors. The permeable polymer layer can increase the effective screening length immediately adjacent to the device surface and thereby enable real-time detection of biomolecules in high-ionic-strength solutions...
December 5, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27930319/co-synthesized-from-the-central-one-carbon-pool-as-source-for-the-iron-carbonyl-in-o2-tolerant-nife-hydrogenase
#15
Ingmar Bürstel, Elisabeth Siebert, Stefan Frielingsdorf, Ingo Zebger, Bärbel Friedrich, Oliver Lenz
Hydrogenases are nature's key catalysts involved in both microbial consumption and production of molecular hydrogen. H2 exhibits a strongly bonded, almost inert electron pair and requires transition metals for activation. Consequently, all hydrogenases are metalloenzymes that contain at least one iron atom in the catalytic center. For appropriate interaction with H2, the iron moiety demands for a sophisticated coordination environment that cannot be provided just by standard amino acids. This dilemma has been overcome by the introduction of unprecedented chemistry-that is, by ligating the iron with carbon monoxide (CO) and cyanide (or equivalent) groups...
December 5, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27929588/use-of-%C3%AE-cyclodextrin-tethered-cationic-polymer-based-fluorescence-enhancement-of-pyrene-and-hybridization-chain-reaction-for-the-enzyme-free-amplified-detection-of-dna
#16
Chunxia Song, Bingjie Li, Xiaohai Yang, Kemin Wang, Qing Wang, Jianbo Liu, Jin Huang
Herein, we proposed an enzyme-free strategy for the amplified detection of DNA by combining the efficient fluorescence enhancement capability of a β-cyclodextrin-tethered cationic polymer (cationic polyβ-CD) to pyrene with the amplification capability of target DNA triggered hybridization chain reaction (HCR). Cationic polyβ-CD with positive charge was synthesized. Two hairpin probes, H1 and H2, were employed in the system and the pyrene-labelled H2 was chosen as the signal unit. The pyrene attached on the sticky end of H2 was flexible and there was strong electrostatic interaction between cationic polyβ-CD and negatively-charged H2, so pyrene could easily enter the cavity of CD that is tethered on the cationic polymer, accompanied by significant fluorescence enhancement...
December 8, 2016: Analyst
https://www.readbyqxmd.com/read/27929401/electrical-impedance-monitoring-of-c2c12-myoblast-differentiation-on-an-indium-tin-oxide-electrode
#17
Ilhwan Park, Yeonhee Hong, Young-Hoo Jun, Ga-Yeon Lee, Hee-Sook Jun, Jae-Chul Pyun, Jeong-Woo Choi, Sungbo Cho
Electrical cell-substrate impedance sensing is increasingly being used for label-free and real-time monitoring of changes in cell morphology and number during cell growth, drug screening, and differentiation. In this study, we evaluated the feasibility of using ECIS to monitor C2C12 myoblast differentiation using a fabricated indium tin oxide (ITO) electrode-based chip. C2C12 myoblast differentiation on the ITO electrode was validated based on decreases in the mRNA level of MyoD and increases in the mRNA levels of myogenin and myosin heavy chain (MHC)...
December 5, 2016: Sensors
https://www.readbyqxmd.com/read/27929071/methionine-sulfoxides-in-serum-proteins-as-potential-clinical-biomarkers-of-oxidative-stress
#18
Satoko Suzuki, Yoshio Kodera, Tatsuya Saito, Kazumi Fujimoto, Akari Momozono, Akinori Hayashi, Yuji Kamata, Masayoshi Shichiri
Oxidative stress contributes to the pathophysiology of a variety of diseases, and circulating biomarkers of its severity remains a topic of great interest for researchers. Our peptidomic strategy enables accurate and reproducible analysis of circulating proteins/peptides with or without post-translational modifications. Conventional wisdom holds that hydrophobic methionines exposed to an aqueous environment or experimental handling procedures are vulnerable to oxidation. However, we show that the mass spectra intensity ratio of oxidized to non-oxidized methionine residues in serum tryptic proteins can be accurately quantified using a single drop of human serum and give stable and reproducible results...
December 8, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27928597/effects-of-bacillus-cereus-endospores-on-free-living-protist-growth
#19
Susana S Santos, Niels Bohse Hendriksen, Hans Henrik Jakobsen, Anne Winding
We studied the predator-prey interactions between heterotrophic protists and endospores of Bacillus cereus group bacteria, in order to gain insight on survival and dispersal of B. cereus endospores in the environment. It has been hypothesised that the spore stage protects against digestion by predating protists. Therefore, experiments were carried out to investigate the impact of B. cereus endospores and vegetative cells, as the only food source, on individual amoeboid, flagellated and ciliated protists. The presence of fluorescent-labelled intracellular bacteria confirmed that B...
December 7, 2016: Microbial Ecology
https://www.readbyqxmd.com/read/27926840/calcium-dependent-structural-dynamics-of-a-spin-labeled-ryr-peptide-bound-to-calmodulin
#20
Cheng Her, Jesse E McCaffrey, David D Thomas, Christine B Karim
We have used chemical synthesis, electron paramagnetic resonance (EPR), and circular dichroism to detect and analyze the structural dynamics of a ryanodine receptor (RyR) peptide bound to calmodulin (CaM). The skeletal muscle calcium release channel RyR1 is activated by Ca(2+)-free CaM and inhibited by Ca(2+)-bound CaM. To probe the structural mechanism for this regulation, wild-type RyRp and four spin-labeled derivatives were synthesized, each containing the nitroxide probe 2,2,6,6-tetramethyl-piperidine-1-oxyl-4-amino-4-carboxylic acid substituted for a single amino acid...
December 6, 2016: Biophysical Journal
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